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1.
Goldstein N 《Biochemistry. Biokhimii?a》2002,67(2):161-170
In this review evidence for the presence of the anion radical
in atmospheric air is considered, and the biological activity of superoxide and negative air ions is compared. Various aspects of the biological effect of superoxide and other reactive oxygen species contained in air at the cell, tissue, and organism levels are discussed. The results of the therapeutic use of exogenous gaseous superoxide and low doses of H2O2 for the treatment of bronchial asthma, pain, and Parkinson's disease are reported. A hypothesis on the mechanism of physiological action of exogenous reactive oxygen species is discussed. 相似文献
2.
B. Culik A. J. Woakes D. Adelung R. P. Wilson N. R. Coria H. J. Spairani 《Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology》1990,160(1):61-70
Summary The energy requirements of Adélie penguin (Pygoscelis adeliae) chicks were analysed with respect to body mass (W, 0.145–3.35 kg, n=36) and various forms of activity (lying, standing, minor activity, locomotion, walking on a treadmill). Direct respirometry was used to measure O2 consumption (
) and CO2 production. Heart rate (HR, bpm) was recorded from the ECG obtained by both externally attached electrodes and implantable HR-transmitters. The parameters measured were not affected by hand-rearing of the chicks or by implanting transmitters. HR measured in the laboratory and in the field were comparable. Oxygen uptake ranged from
in lying chicks to
at maximal activity, RQ=0.76. Metabolic rate in small wild chicks (0.14–0.38 kg) was not affected by time of day, nor was their feeding frequency in the colony (Dec 20–21). Regressions of HR on
were highly significant (p< 0.0001) in transmitter implanted chicks (n=4), and two relationships are proposed for the pooled data, one for minor activities (
), and one for walking (
). Oxygen consumption, mass of the chick (2–3 kg), and duration of walking (T, s) were related as
, whereas mass-specific O2 consumption was related to walking speed (S, m·s-1) as
.Abbreviations
bpm
beats per minute
-
D
distance walked (m)
-
ECG
electrocardiogram
-
HR
heart rate (bpm)
-
ns
number of steps
-
RQ
respiratory quotient
-
S
walking speed (m·s-1)
-
T
time walked (s)
-
W
body mass (kg) 相似文献
3.
High groundwater nitrate concentrations inhibit eutrophication of sulphate-rich freshwater wetlands 总被引:2,自引:0,他引:2
E.C.H.E.T. Lucassen A.J.P. Smolders A.L. van der Salm J.G.M. Roelofs 《Biogeochemistry》2004,67(2):249-267
During the last 60 years, pollution of the groundwater with
has greatly increased in many parts of Europe, as a consequence of excessive use of manure and synthetic fertilisers. Monitoring of groundwater-fed wetlands indicated that sediments with high
concentrations had the lowest Fe and
concentrations in the pore water. A comparison of two restored open water fens, differing in
supply via the groundwater, indicated that the redox potential and the sulphate (
) reduction rate were lower when the groundwater contained not only
but also high
concentrations. The lower
reduction rates in the
-rich open water fen were associated with lower
concentrations and the presence of plant species characteristic of clear water. In contrast, the higher
reduction rates in the
-poor open water fen were associated with very high
concentrations and massive development of plant species characteristic of eutrophic environments. Investigations at
-rich seepage sites in black alder carrs, showed that high
concentrations in the pore water caused chlorosis in the alder carr vegetation, due to lower availability of Fe in the pore water and less Fe uptake by the plants. Experimental desiccation of sediments proved that the
-rich seepage sites contained no oxidisable FeS
x
, contrary to
-poor locations, which became acidified and mobilised extremely high amounts of
due to FeS
x
oxidation. A laboratory experiment showed that
addition to sediments led to reduced releases of Fe,
and S2–, very likely due to the oxidation of reduced Fe and S compounds. Overall, the results confirmed that
is an energetically more favourable electron acceptor in anaerobic sediments than Fe and
, and that high
loads function as a redox buffer, preventing reduction of Fe and
. Limited
reduction prevents S2– -mediated mobilisation of
from Fe-
complexes. At a higher redox potential, reduced Fe, including FeS
x
, was oxidised, increasing the content of Fe(III) capable of binding
. This prevented increased
availability and the concomitant massive development of plant species characteristic of eutrophic environments. 相似文献
4.
The effect of inhibitors of the cytochrome pathway and alternative oxidase on the rate of respiration and generation of reactive oxygen species by pea mitochondria was studied. Respiration of mitochondria from pea cotyledons was inhibited by 70-80% by salicylhydroxamate (SHAM). The rate of hydrogen peroxide production by pea cotyledon mitochondria during succinate oxidation was 0.15 nmol/min per mg protein. SHAM considerably accelerated the hydrogen peroxide production. The SHAM-dependent H2O2 production was stimulated by 2 M antimycin A and inhibited by 5 mM KCN and 1 M myxothiazol. The study of the rate of
generation by pea mitochondria using EPR spin traps and epinephrine oxidation showed that H2O2 accumulation can be accounted for by a significant increase in the rate of
production. 相似文献
5.
Besides major NADH-, succinate-, and other substrate oxidase reactions resulting in four-electron reduction of oxygen to water, the mitochondrial respiratory chain catalyzes one-electron reduction of oxygen to superoxide radical
followed by formation of hydrogen peroxide. In this paper the superoxide generation by Complex I in tightly coupled bovine heart submitochondrial particles is quantitatively characterized.The rate of superoxide formation during
-controlled respiration with succinate depends linearly on oxygen concentration and contributes approximately 0.4% of the overall oxidase activity at saturating (0.25 mM) oxygen. The major part of one-electron oxygen reduction during succinate oxidation (80%) proceeds via Complex I at the expense of its
-dependent reduction (reverse electron transfer). At saturating NADH the rate of
formation is substantially smaller than that with succinate as the substrate. In contrast to NADH oxidase,the rate-substrate concentration dependence for the superoxide production shows a maximum at low (50 µM)concentrations of NADH. NAD+ and NADH inhibit the succinate-supported superoxide generation. Deactivation of Complex I results in almost complete loss of its NADH-ubiquinone reductase activity and in increase in NADH-dependent superoxide generation. A model is proposed according to which complex I has two redox active nucleotide binding sites.One site (F) serves as an entry for the NADH oxidation and the other one (R) serves as an exit during either the succinate-supported NAD+ reduction or superoxide generation or NADH-ferricyanide reductase reaction.Translated from Biokhimiya, Vol. 70, No. 2, 2005, pp. 150–159.Original Russian Text Copyright © 2005 by Vinogradov, Grivennikova.This revised version was published online in April 2005 with corrections to the post codes. 相似文献
6.
Direct nonenzymatic oxidation of semiquinone by oxygen is one of the main sources of superoxide radicals
in mitochondria. Using all the known data on hepatocyte mitochondria, we have revealed the correlation between the rate of superoxide generation by the bc
1complex and the transmembrane potential (). Assuming that the main electrogenic stage of the Qcycle is the electron transfer between the cytochrome bhemes, then the rate of superoxide generation sharply increases when grows from 150 to 180 mV. However, this interrelation is ambiguous. Indeed, the increase of the generation rate with the growth of the potential can occur faster when succinate dehydrogenase is inhibited by malonate than when external ADP is exhausted. When the potential is changed by adding phosphate or potassium (K+), the rate of
production remains constant, although the comparison of the rates at the same reveals the effect of phosphate or potassium. It turned out that the rate of
generation is a function of
rather than any of its components. Phosphate and K+have practically no influence on
, since the change in is compensated by pH. The rate of superoxide generation by the bc
1complex is a multiple function of the electron-transfer activity of enzymes, the processes determining the membrane potential (e.g., loading), and the oxygen concentration. The kinetic model proposed in this work may serve to understand how the superoxide production is regulated. 相似文献
7.
A small catchment on the Swedish West Coast has been studied over four years to determine S dynamics by using S isotope ratios. A Norway spruce dominated forest covers the catchment, and small peat areas occur in the lower parts of the catchment. The runoff
values varied both during the year, and from year to year. Over the period from February 1990 to December 1993, the
values ranged from — 1%. to +11%. Over the same period, the throughfall
values ranged from +1%. to +15%. There was no correlation (r
2= 0.01; Pr(F)=0.57) between
values in throughfall and runoff. Since the only input of S to the catchment is atmospheric deposition, the long-term runoff S mass flux is controlled by the deposition. Therefore, processes in the catchment are responsible for the variation in the runoff
values. During periods with
enriched runoff, bacterial dissimilatory SO
4
2–
reduction occurs in the catchment. After very dry periods, oxidation of this reduced S, which is32S-enriched, can be traced in runoff. Previous studies of the catchment have not been able to distinguish between: 1) oxidation of reduced S and dry deposition, and 2) reduction and adsorption. From the current study, it can be concluded that adsorption and dry deposition cannot cause the observed variation in runoff
. 相似文献
8.
D. L. Evans R. J. Rose 《Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology》1988,157(6):791-799
Summary Six Standardbred horses were used to evaluate the time course of pulmonary gas exchange, ventilation, heart rate (HR) and acid base balance during different intensities of constant-load treadmill exercise. Horses were exercised at approximately 50%, 75% and 100% maximum oxygen uptake (
max) for 5 min and measurements taken every 30 s throughout exercise. At all work rates, the minute ventilation, respiratory frequency and tidal volume reached steady state values by 60 s of exercise. At 100%
max, the oxygen consumption (
) increased to mean values of approximately 130 ml/kg·min, which represents a 40-fold increase above resting
. At the low and moderate work rates,
showed no significant change from 30 s to 300 s of exercise. At the high work rate, the mean
at 30 s was 80% of the value at 300 s. The HR showed no significant change over time at the moderate work rate but differing responses at the low and high work rates. At the low work rate, the mean HR decreased from 188 beats/min at 30 s to 172 beats/min at 300 s exercise, whereas at the high work rate the mean HR increased from 204 beats/min at 30 s to 221 beats/min at 300 s exercise. No changes in acid base status occurred during exercise at the low work rate. At the moderate work rate, a mild metabolic acidosis occurred which was nonprogressive with time, whereas the high work rate resulted in a progressive metabolic acidosis with a base deficit of 16 mmol/l by 300 s exercise. It is concluded that the kinetics of gas exchange during exercise are more rapid in the horse than in man, despite the relatively greater change in
in the horse when going from rest to high intensity exercise.Symbols and abbreviations E
minute ventilation
-
V
T
tidal volume
-
oxygen uptake
-
carbon dioxide output
-
oxygen pulse
-
ventilatory equivalent for oxygen
-
ventilatory equivalent for carbon dioxide
- R
respiratory exchange ratio
- HR
heart rate
- SBC
standard bicarbonate
- STPD
standard temperature and pressure dry
- BTPS
body temperature and pressure saturated
-
arterial oxygen content
-
arteriovenous oxygen content difference
- Rf
respiratory frequency 相似文献
9.
Behrenfeld Michael J. Prasil Ondrej Kolber Zbigniew S. Babin Marcel Falkowski Paul G. 《Photosynthesis research》1998,58(3):259-268
Exposure of algae or higher plants to bright light can result in a photoinhibitory reduction in the number of functional PS II reaction centers (n) and a consequential decrease in the maximum quantum yield of photosynthesis. However, we found that light-saturated photosynthetic rates (Pmax) in natural phytoplankton assemblages sampled from the south Pacific ocean were not reduced despite photoinhibitory decreases in n of up to 52%. This striking insensitivity of Pmax to photoinhibition resulted from reciprocal increases in electron turnover (
)through the remaining functional PS II centers. Similar insensitivity of Pmax was also observed in low light adapted cultures of Thalassiosira weissflogii (a marine diatom), but not in high light adapted cells where Pmax decreased in proportion to n. This differential sensitivity to decreases in n occurred because
was close to the maximum achievable rate in the high light adapted cells, whereas
was initially low in the low light adapted cells and could thus increase in response to decreases in n. Our results indicate that decreases in plant productivity are not necessarily commensurate with photoinhibition, but rather will only occur if decreases in n are sufficient to maximize
or incident irradiance becomes subsaturating. 相似文献
10.
The tetrameric heart isozyme of lactate dehydrogenase (H4) is modified by p-chloromercuribenzoate (PCMB) to produce the inactive tetramer
and then hybridized with native tetrameric muscle isozyme (M4). The hybrid mixture
was isolated by polyacrylamide gel electrophoresis (PAGE) and then stained for enzyme activity and with Coomassie brilliant blue. Only three bands were found on the gels in either case. The hybrid enzymes
as isolated by PAGE have half the specific activity of the native muscle enzyme. The electrophoresis properties of HM3 are very similar to those of HM3, while the electrophoresis properties of
are very similar to those of H2M2. The above results strongly suggest that the tetramer having enzymatic activity contains at least two native subunits, and the di-subunit in the tetrameric enzyme is the minimal functional unit. 相似文献
11.
Pierre Dejours Jean-Paul Truchot 《Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology》1988,158(3):387-391
Summary In the intertidal shore crab,Carcinus maenas, pH and
values of the prebranchial venous hemolymph,
and
, the PO2 values of the arterialized cardiac hemolymph,
, were measured, and the ventilatory activity was assessed by measuring the hydrostatic pressures at the exits of the epibranchial cavities, under four environmental conditions: normoxic water, normoxic air, hypoxic gas, hyperoxic gas.In the crab breathing normoxic air,
was lower and
higher than in animals breathing normoxic water. With the switch to hypoxic gas, ventilation increased and
and
decreased. With the switch to hyperoxic gas, ventilation decreased,
and
increased and
decreased.Thus these crabs breathing air were not as well oxygenated as when breathing air-equilibrated water, and because of their low
, they were relatively hypervetilating and hypocapnic compared to air-breathing vertebrates. Hyperoxic breathing, increasing
and reducing ventilatory drive, led to increased
. Conversely,
was reduced by hypoxic breathing. These observations suggest that the gas exchanger of intertidal crabs is not as successfully designed for air breathing as that of land-colonizing insects and air-breathing vertebrates. 相似文献
12.
Boniface S. Moses 《Environmental Biology of Fishes》2001,61(1):99-109
This paper investigates the relationship between the hydroclimatic parameters (rainfall and flood index) and the catch, stock abundance and recruitment of the catfish, Chrysichthys nigrodigitatus (Bagridae) and the bonga, Ethmalosa fimbriata (Clupeidae) of southeastern Nigeria's inshore waters. For C. nigrodigitatus, most peaks in the mean biomass
and recruitment
curves occurred during the 'wet' years, i.e., years for which the percentage deviations of rainfall
and flood index
from their means remained above their averages. Catch and abundance respectively showed good positive linear correlation with the flood index. E. fimbriata behaved differently; some peaks in the
and
curves occurred in the 'wet' and some in the 'dry' years; and there was no correlation between the annual catch of bonga and either the rainfall or the flood index. The hypothesis, that linear relationships exist between the interannual variations in the hydroregime and the yearly fluctuations in the catch and population structure of some coastal and estuarine fishes, holds true for the catfish, C. nigrodigitatus, but not for bonga, E. fimbriata. 相似文献
13.
P. Pic 《Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology》1978,123(2):155-162
Summary In seawater (SW)-adaptedMugil andFundulus, gill effluxes of Na+
and of Cl–
and the simultaneously recorded transgill potential (P.D.) differ according to whether they are measured in stressed or rested animals.In rested animals of the two species, transfer to Ringer's solution considerably reduces the P.D. but not
. InFundulus,
is also decreased. Transfer of the two species from SW to fresh water (FW) reduces
and
by 75 to 85% and leads to a large inversion of P.D. When K+ is added to FW, a gill depolarization occurs, as well as a large increase of
and
.These results suggest that: 1) the P.D. originates primarily from the diffusion of cations, the gill permeability to Na+ (
) being greater than that to Cl– (
), 2) a Cl–/Cl– exchange independent of P.D. is associated with the Cl– pump; 3) Cl– pump activity is linked to Na+/K+ exchange which in turn is associated to a Na+/Na+ exchange diffusion mechanism.In stressed individuals of the two species, the P.D. in SW, as well as the P.D. changes observed during transfer experiments, are considerably reduced. The decrease of
and
observed after transfer from SW to FW are also minimised. Changes are smaller inFundulus. The decrease of P.D. characterizing stressed animals may be at least in part due to a 3 to 4 fold increase of
which becomes equal to
in both species.As a result of stress, the K+-activated Na+ and Cl– excretion mechanisms are totally inhibited inFundulus and partially so inMugil.Stress response seems more intense inFundulus and recovery from stress faster inMugil. 相似文献
14.
Douglas A. Burns 《Biogeochemistry》1998,40(1):73-96
Models of the effects of atmosphericN deposition in forested watersheds have notadequately accounted for the effects of aquatic andnear-stream processes on the concentrations and loadsof NO
in surface waters. This studycompared the relative effects of aquatic andnear-stream processes with those from the terrestrialecosystem on the retention and transport ofNO
in two contrasting stream reaches ofthe Neversink River, a forested watershed in theCatskill Mountains of New York that receives among thehighest load of atmospheric N deposition in thenortheastern United States. Stream water samples werecollected every two hours and ground-water andtributary samples were collected daily at base flowconditions during four 48-hour periods from April toOctober 1992, and NO
mass balances werecalculated for each site. Results indicated diurnalvariations in stream NO
concentrations inboth reaches during all four sampling periods; this isconsistent with uptake of NO
byphotoautotrophs during daylight hours. Mass-balanceresults revealed significant stream reach losses ofNO
at both sites during all samplingperiods. The diurnal variations in NO
concentrations and the retention of NO
relative to terrestrial contributions to the streamreaches were greater downstream than upstream becausephysical factors such as the head gradients ofinflowing ground water and the organic matter contentof sediment are more favorable to uptake anddenitrification downstream. The mass retention ofNO
increased as the mean 48-hr streamdischarge increased at each site, indicating that theresponsible processes are dependent onNO
supply. Low stream temperatures duringthe April sampling period, however, probably reducedthe rate of retention processes, resulting in smallerlosses of NO
than predicted from streamdischarge alone. Water samples collected from thestream, the hyporheic zone, and the alluvial groundwater at sites in both reaches indicated that the neteffect of hyporheic processes on downstreamNO
transport ranged from conservativemixing to complete removal by denitrification. Therelative effects of biological uptake anddenitrification as retention mechanisms could not bequantified, but the results indicate that bothprocesses are significant. These results generallyconfirm that aquatic and near-stream processes causesignificant losses of NO
in the NeversinkRiver, and that the losses by these processes atdownstream locations can exceed the NO
contributions to the stream from the terrestrialenvironment during summer and fall base-flowconditions. Failure to consider these aquatic andnear-stream processes in models of watershed responseto atmospheric N deposition could result inunderestimates of the amount of NO
leaching from forested ecosystems and to an inabilityto unequivocally relate geographic differences inNO
concentrations of stream waters tocorresponding differences in terrestrial processes. 相似文献
15.
Chinmay K. Mukhopadhyay Mrinal K. Ghosh Indu B. Chatterjee 《Molecular and cellular biochemistry》1995,142(1):71-78
It has recently been indicated that in the absence of free iron, NADPH initiates oxidative damage of proteins in guinea pig liver microsomes and also lipid peroxidation and protein damage in cardiac microsomes and that ascorbic acid specifically inhibits both the lipid peroxidation and protein damage [Mukhopadhyay CK, Chatterjee IB: J Biol Chem 269: 13390–13397, 1994; Mukhopadhyay Met al.: Mol Cell Biochem 126: 69–75, 1993]. In this paper we demonstrate that Fe(III)-independent NADPH-initiated lipid peroxidation and oxidative damage of proteins occur in the microsomes of all the extrahepatic tissues including lung, kidney, adrenal gland and brain and that both the lipid peroxidation and protein damage are specifically prevented by ascorbic acid. We further demonstrate that when NADPH is replaced by
as the electron donor, the
lipid peroxidation and protein damage are also inhibited by ascorbic acid.Abbreviations AH2
ascorbic acid
- SOD
bovine erythrocyte superoxide dismutase
- GSH
glutathione
- XOD
xanthine oxidase
- cyt P450
cytochrome P450
- DFO
desferrioxamine 相似文献
16.
B. Grubb G. E. Folk Jr. 《Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology》1978,128(2):185-188
Summary The rate of oxygen consumption (
) by skeletal muscle was investigated in isolated perfused hindlimbs of laboratory rats and lemmings (Lemmus). In both species,
increased in proportion to blood flow rate, even at flow rates 4–5 times above resting level. The slope of the line relating
to skeletal muscle blood flow was significantly greater in the lemming than in the rat. This may be related to the inverse relationship between body weight and metabolic rate. These data support the hypothesis that in small animals a dependent relationship exists between blood flow and skeletal muscle
. 相似文献
17.
Regulation of mineral nitrogen uptake in plants 总被引:15,自引:0,他引:15
In the biosphere plants are exposed to different forms of N, which comprise mineral and organic N forms in soils as well as gaseous NH3, NOx, and molecular N2 in the atmosphere. The form of N uptake is mainly determined by its abundance and accessibility, which make
and
the most important N forms for plant nutrition under agricultural conditions. With minor importance, the form of N uptake is also subject to plant preferences, by which plants maintain their cation/anion balance during uptake. However, some species seem to have an obligatory preference which even prevents their growth on certain other N sources. In general, uptake of a certain N form closely matches the growth-related demand of the plant, at least when N transport to the root surface is not limiting. In addition, many plants accumulate large pools of N during vegetative growth which are remobilized in the generative stage. As a consequence, systems responsible for N transport need to be tightly regulated in their expression and activity upon sensing N availability and plant demand. Employing the tools of molecular genetics, the first plant genes encoding transporters for inorganic N have recently been isolated and characterized. These data can now complete the wealth of physiological and nutritional studies on N uptake. The present article will focus on the uptake of
and
into root cells and tries to link data derived from physiological, genetic and molecular studies. 相似文献
18.
Jack P. Hayes 《Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology》1989,159(4):453-459
Summary I compared the maximal aerobic metabolic rates (
), field metabolic rates (FMR), aerobic reserves (
-FMR), and basal metabolic rates (BMR) of wild and recently captured deer mice from low (440 m) and high (3800 m) altitudes. To separate the effects of the thermal environment from other altitudinal effects, I examined mice from different altitudes, but similar thermal environments (i.e., summer mice from high altitude and winter mice from low altitude). When the thermal environment was similar,
, FMR, and aerobic reserve of low and high altitude mice did not differ, but BMR was significantly higher at high altitude. Thus, in the absence of thermal differences, altitude had only minor effects on the aerobic metabolism of wild or recently captured deer mice.At low altitude, there was significant seasonal variation in
, FMR, and aerobic reserve, but not BMR. BMR was correlated with
, but not with FMR. The significant positive correlation of BMR with
indicates a cost of high
, because higher BMR increases food requirements and energy use during periods of thermoneutral conditions.Abbreviations
BMR
basal metabolic rate
-
FMR
field metabolic rate
-
partial pressure of oxygen
-
T
a
ambient temperature
-
T
b
body temperature
-
T
e
operative temperature
-
maximal aerobic metabolic rate 相似文献
19.
Gregory K. Snyder Wesley W. Weathers 《Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology》1977,117(3):291-301
Summary Resting rates of O2 consumption
against
, exercise endurance times and
during recovery from vigorous exercise were measured inSceloporus occidentalis captured near sea level and inS. graciosus captured above 2850 m. Oxygen consumption against
was also measured inS. occidentalis captured above 2850 m. When
was recorded continuously, as ambient
was slowly reduced from 155 Torr, it became directly dependent upon ambient
between 110 and 120 Torr. The critical
for the high altitude lizards was lower than that for the lowland lizards, which enabled the former to maintain relatively higher
's when ambient
was reduced below 120 Torr. The high altitude lizards also had significantly greater endurance when stimulated to exercise at 1600 m (
130 Torr). Both the higher
under hypoxia and the greater endurance roughly parallel a significantly greater maximum
in the high altitude lizards. At a simulated altitude of 3600 m (
100 Torr), maximum
and rate of recovery of the O2 debt calculated from post active
were significantly reduced in the lowland but not the high altitude lizards. The effects of simulated altitude conditions on the lowland but not the mountaine animals indicate adaptations to altitude in these sceloporine lizards. We did not find any consistent relationship between organ/body weight ratios or hematocrit and our measures of
endurance or the altitude at which the lizards were captured. 相似文献
20.
Didier G. Arqués Jean-Paul Fallot Christian J. Michel 《Bulletin of mathematical biology》1998,60(1):163-194
The self-complementary subset
∪{AAA,TTT} with
= {AAC, AAT, ACC, ATC, ATT, CAG, CTC, CTG, GAA, GAC, GAG, GAT, GCC, GGC, GGT, GTA, GTC, GTT, TAC, TTC} of 22 trinucleotides
has a preferential occurrence in the frame 0 (reading frame established by the ATG start trinucleotide) of protein (coding)
genes of both prokaryotes and eukaryotes. The subsets
∪{CCC} and
∪{GGG} of 21 trinucleotides have a preferential occurrence in the shifted frames 1 and 2 respectively (frame 0 shifted by
one and two nucleotides respectively in the 5′-3′ direction).
and
are complementary to each other. The subset
contains the subset
which has the rarity property (6 × 10−8) to be a complementary maximal circular code with two permutated maximal circular codes
and
in the frames 1 and 2 respectively.
is called a C3 code.
A quantitative study of these three subsets
in the three frames 0, 1, 2 of protein genes, and the 5′ and 3′ regions of eukaryotes, shows that their occurrence frequencies
are constant functions of the trinucleotide positions in the sequences. The frequencies of
in the frame 0 of protein genes are 49, 28.5 and 22.5% respectively. In contrast, the frequencies of
in the 5′ and 3′ regions of eukaryotes, are independent of the frame. Indeed, the frequency of
in the three frames of 5′ (respectively 3′) regions is equal to 35.5% (respectively 38%) and is greater than the frequencies
and
, both equal to 32.25% (respectively 31%) in the three frames.
Several frequency asymmetries unexpectedly observed (e.g. the frequency difference between
and
in the frame 0), are related to a new property of the subset
involving substitutions. An evolutionary analytical model at three parameters (p, q, t) based on an independent mixing of the 22 codons (trinucleotides in frame 0) of
with equiprobability (1/22) followed by t ≈ 4 substitutions per codon according to the proportions p ≈ 0.1; q ≈ 0.1 and r = 1 − p − q ≈ 0.8 in the three codon sites respectively, retrieves the frequencies of
observed in the three frames of protein genes and explains these asymmetries. Furthermore, the same model (0.1, 0.1, t) after t ≈ 22 substitutions per codon, retrieves the statistical properties observed in the three frames of the 5′ and 3′ regions.
The complex behaviour of these analytical curves is totally unexpected and a priori difficult to imagine. 相似文献